This module uses the FakII suite of programs to perform shotgun
assembly. Output will be placed in the fofn.assembly directory, where fofn
is the filename prefix listed in the "Files to Process" panel. The output is
in a format suitable for directed assembly within gap4. This can also be
performed by using the "Enter Assembly into Gap4" module.

Option: E limit

Option: D limit

Option: O threshold

These parameters control the graph component of FakII, which is used to
find the initial overlaps between sequences.
For further details, seesection Assembly FAKII.

Option: Auto-generate constraints

When enabled, this uses the reading direction (forward / reverse primers),
the template name and the insert size, to produce a file containing data to
constrain how the readings may be assembled.

Option: E rate

Option: O threshold

Option: D threshold

These parameters control the assemble component of FakII, which is used
for determining the best construction of sequences from the overlap graph.

Option: Assembly number

This allows for non optimum assemblies to be chosen. The optimum assembly is
assembly number 1, with the next optimum being number 2, and so on.

This page is maintained by
staden-package.
Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/pregap4_unix_42.html